pypomp.models.UKMeasles

class pypomp.models.UKMeasles[source]

Bases: object

Class interface for building UK Measles POMP models and accessing data.

This class constructs POMP models based on the He et al. 2010 [1] formulation and accesses epidemiological case reports data from Korevaar et al. 2020 [2].

Model Variants

The following sub-models (selected via the model parameter in Pomp() and PanelPomp()) are available:

  • “001”: Standard He10 model (He et al. 2010 [1]) including mixing parameter alpha and death rate mu.

  • “001b” (Default): He10 model without alpha (mixing parameter fixed to 1) and without mu (death rate parameter omitted).

  • “001d”: He10 model without alpha or mu (similar to “001b”), but configured with gradient-stable transitions and measurement densities for DPOP training.

  • “002”: He10 model without alpha or mu, where the transmission import rate iota scales with population size: iota = exp(iota1 + iota2 * log(pop)). Designed for shared parameter panel modeling.

  • “002d”: DPOP-enabled version of “002” combining the population-scaling iota parameterization with gradient-stable transitions/measurement densities.

  • “003”: Variant of the He10 model formulated with a continuous process model.

Model Parameters

R0float

Basic reproduction number.

  • Active Models: All models.

  • Estimation Scale: Log transformed.

sigmafloat

Rate of transition from susceptible to exposed (1/latent period).

  • Active Models: All models.

  • Estimation Scale: Log transformed.

gammafloat

Rate of transition from exposed to infectious (1/infectious period).

  • Active Models: All models.

  • Estimation Scale: Log transformed.

iotafloat

Daily imported cases rate.

  • Active Models: “001”, “001b”, “001d”, “003” (omitted in “002”, “002d”).

  • Estimation Scale: Log transformed.

iota1float

Baseline imported cases (used in population-scaling import rate formulation).

  • Active Models: “002”, “002d” (replaces iota).

  • Estimation Scale: Untransformed (natural scale).

iota2float

Rate at which imported cases increase with log population size.

  • Active Models: “002”, “002d” (replaces iota).

  • Estimation Scale: Untransformed (natural scale).

sigmaSEfloat

Rate of stochastic extrademographic variation / process noise.

  • Active Models: All models.

  • Estimation Scale: Log transformed.

cohortfloat

Cohort effect coefficient reflecting entry rate of children into school.

  • Active Models: All models.

  • Estimation Scale: Logit transformed.

amplitudefloat

Seasonality amplitude coefficient of transmission rate.

  • Active Models: All models.

  • Estimation Scale: Logit transformed.

rhofloat

Reporting probability.

  • Active Models: All models.

  • Estimation Scale: Logit transformed.

psifloat

Reporting error over-dispersion.

  • Active Models: All models.

  • Estimation Scale: Log transformed.

mufloat

Background death rate.

  • Active Models: “001” only.

  • Estimation Scale: Log transformed.

alphafloat

Mixing parameter/exponent for force of infection (e.g. transmission rate scales with (I + iota)**alpha).

  • Active Models: “001” only.

  • Estimation Scale: Log transformed.

S_0, E_0, I_0, R_0float

Initial proportions of susceptible, exposed, infectious, and recovered populations.

  • Active Models: All models.

  • Estimation Scale: Transformed as log ratio proportions (normalized relative to sum).

References

Methods

AK_mles()

Returns a data frame of Aaron King's MLEs from https://kingaa.github.io/sbied/measles/index.html

PanelPomp(units, theta[, model, ...])

Returns a PanelPomp object for the UK Measles data.

Pomp(unit, theta[, model, interp_method, ...])

Returns a Pomp object for the UK Measles data.

subset([units, clean])

Return a subset of the UKMeasles data, filtered by the given units.

units()

List of all unique unit names in the UKMeasles dataset.